Hi,
Could you send me off-list the topology, input coordinates, and 1
frame of the trajectory in question so I can reproduce on this end?
Thanks.
-Dan
On Thu, Aug 8, 2013 at 10:48 AM, VanDyne_Aaron
<VanDyne_Aaron.roberts.edu> wrote:
> I ran the check command, and no bad overlaps were found. The trajectory has the same coordinates as the .prmcrd file, which gives a realistic number when used with the default imin.
>
> -Aaron van Dyne
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Thursday, August 08, 2013 11:27 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Trajectory post-processing
>
> Hi,
>
> On Thu, Aug 8, 2013 at 8:39 AM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>> AMBER has now been updated on the supercomputer, but I am still having the same problem.
>
> Did you ever run the 'check' command in cpptraj/ptraj to look for bad
> overlaps in the trajectory that is giving you the large VDW energy?
>
>> On Tue, Aug 6, 2013 at 2:50 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu> wrote:
>>> The outputted energies always have a van der Waals contribution that is on the order of 10^16.
>
>> This indicates you have a clash somewhere in your trajectory file. Use
>> the 'check' command in cpptraj or ptraj to see if there are any bad
>> overlaps.
>
> -Dan
>
>>
>> -Aaron van Dyne
>> ________________________________________
>> From: Jason Swails [jason.swails.gmail.com]
>> Sent: Tuesday, August 06, 2013 8:13 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Trajectory post-processing
>>
>> On Tue, Aug 6, 2013 at 5:59 PM, VanDyne_Aaron <VanDyne_Aaron.roberts.edu>wrote:
>>
>>> I am using Amber 12. I do not know which bug fixes have been applied (I am
>>> running on the University of Pittsburgh Department of Computational and
>>> Systems Biology computing cluster. I would imagine all the appropriate bug
>>> fixes have been applied).
>>>
>>
>> You can find out with the command
>>
>> $AMBERHOME/update_amber --version
>>
>> The assumption that supercomputers keep their installations up-to-date is
>> rarely a good one. Since they are not regular users, they probably update
>> only when requested.
>>
>> You can use the command:
>>
>> $AMBERHOME/update_amber --check
>>
>> to see if there are available updates.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
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>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Aug 09 2013 - 08:30:05 PDT
